September 30, 2010

Y-chromosomes of Filipino Negritos and non-Negritos

European Journal of Human Genetics (29 September 2010) | doi:10.1038/ejhg.2010.162

The Y-chromosome landscape of the Philippines: extensive heterogeneity and varying genetic affinities of Negrito and non-Negrito groups

Frederick Delfin et al.

The Philippines exhibits a rich diversity of people, languages, and culture, including so-called ‘Negrito’ groups that have for long fascinated anthropologists, yet little is known about their genetic diversity. We report here, a survey of Y-chromosome variation in 390 individuals from 16 Filipino ethnolinguistic groups, including six Negrito groups, from across the archipelago. We find extreme diversity in the Y-chromosome lineages of Filipino groups with heterogeneity seen in both Negrito and non-Negrito groups, which does not support a simple dichotomy of Filipino groups as Negrito vs non-Negrito. Filipino non-recombining region of the human Y chromosome lineages reflect a chronology that extends from after the initial colonization of the Asia-Pacific region, to the time frame of the Austronesian expansion. Filipino groups appear to have diverse genetic affinities with different populations in the Asia-Pacific region. In particular, some Negrito groups are associated with indigenous Australians, with a potential time for the association ranging from the initial colonization of the region to more recent (after colonization) times. Overall, our results indicate extensive heterogeneity contributing to a complex genetic history for Filipino groups, with varying roles for migrations from outside the Philippines, genetic drift, and admixture among neighboring groups.

25 comments:

That map cannot be right: it's full of gray "other", and that means Y(xC,K), what in Eurasia can only mean DE or F(xK), neither of which has been reported at meaningful levels in Island SE Asia, much less Papua.

There must be an error with the coloring. The Filipino inset seems correct though.

C (C2?) and K (MNOPS) are Negrito clades. From what I recall also present in Melanesia and Wallacea and should correspond with the oldest crossing(s) of Wallace Line and the straits West of Philippines, maybe as early as the Middle Paleolithic.

O1a and O1a2 are specifically Austronesian clades, found in Taiwan Aborigines and Filipinos in great apportions.

Other O clades, mostly O3, must have other pre-Austronesian origin. In Philippines, O3* in particular is found among Southern Malay Filipinos and two Negrito groups, one of them from further North (Iraya). O3a3b seems related to North Filipinos but not Taiwan Aborigines.

Malay Filipinos seem divided in three clusters: North, West/Center and South. The Southern cluster looks the less Austronesian because of the high O3* (and some K and C); the Western cluster is dominated by O1a2, except the Hanunuo, who actually appear "Negrito" with all that K, while the Northern cluster is more diverse (O1a*, O1a2 and some "pre-Austronesian" O3a3b).

Which ones are associated with Australians? The author doesn't discriminate between any possible various Cs or Ks, yet these are the most likely haplogroups involved. But the C appears to be mostly South Wallacean, prssumably C2. Is it C2 in the Agta? And What K is spread down the western side of the main island? Admittedly the article deals with the Philippines but if they're going to look at the wider picture it's strange that no C appears anywhere in New Guinea or the islands to the north. Or even stranger still, on the Pacific islands.

The maps differentiate between an array of Os, yet they're almost certainly relatively recent arrivals in the Philippines. And what is the NO haplogroup shown in Northern Mindanao (Surigaonon and Manobo)?

On what grounds do you claim that to be the case? O3 is certainly part of the Austronesian expansion into the Pacific. So all Os are present in the Austronesian expansion, although some may have been picked up during the expansion.

"The Southern cluster looks the less Austronesian because of the high O3*"

Could be more Austronesian if it's associated with the eastward movement.

I think the authors didn't feel need to discriminate between branches of K and C because that they are indigenous to the region, so their intense presence in Negrito groups was no surprise for them. But it would have been better if they had further detailed these haplogroups.

"O3 is certainly part of the Austronesian expansion into the Pacific".

Pointless. I am discussing Philippines not that later stage. Obviously the Malayo-Polynesian branch of Austronesians coalesced in the Philippines (or very close) but what I am talking is about the first arrival of Austronesians to Philippines from Taiwan. A fact strongly supported by linguistics (and after all "Austronesian" is a linguistic concept).

If the Indoeuropeans that arrived to America were mostly R1b1b2a1a, that does not mean that R1b1b2a1a is originally Indoeuropean. In fact it is surely not the case.

Can you make a difference between the core population and the expanded population, which may well be very different genetically? Language (and culture, ethnic identity) is much more easy to spread than genes.

"So all Os are present in the Austronesian expansion, although some may have been picked up during the expansion".

Pointless. Messing around with words. Arguing about nothing.

"That is interesting and warrants further investigation".

I don't know much but I stumbled today on this Wikipedia map on main ethnicities in Philippines and the color code seems to follow that same pattern. However the legend does not help to clarify.

A rather odd, but intriguing study. You can find it here. http://www.yourfilelink.com/get.php?fid=577370

On the one hand, they didn't screen for any known sublineages of C and K. On the other hand, they show (Fig. 3) that Negrito and non-Negrito C's are related to Australian and SE Asian ones but apparently not to Polynesian ones. Interestingly, non-Negrito Cs seem to be different from the Negrito C's, coming off from SEAsian C's and BOTH having a connection to Australia. This likely means that Negrito, non-Negrito and Australian aboriginal groups all derive from an ancient SE pool.

On the one hand, they claim "In particular, some Negrito groups are associated with indigenous Australians" but their Fig. 3 shows that non-Negrito groups also have an Australian connection.

On the one hand, they claim "We find extreme diversity in the Y-chromosome lineages of Filipino groups with heterogeneity seen in both Negrito and non-Negrito groups, which does not support a simple dichotomy of Filipino groups as Negrito vs non-Negrito." On the other hand, they remark: "Recently, analysis of about 50 000 SNPs in a wide variety of Asian populations, including several FEN groups, found no clear-cut genetic distinction between FEN and FEnN groups, and concluded that, FEN and FEnN groups were part of the same wave of migration.14 This conclusion seems at odds with both the NRY data, which indicate an earlier presence of haplogroups C-RPS4Y and K-M9 in the Philippines that is associated with FEN groups, and with mtDNA data indicating novel and ancient mtDNA lineages in a FEN group (E Gunnarsdottir and M Stoneking, unpublished data)." Their Table 1 shows that virtually all haplogroups detected in the Philippines, including C and K, are shared between Negrito and Non-Negrito groups.

"I think the authors didn't feel need to discriminate between branches of K and C because that they are indigenous to the region"

They may not be indigenous to the Philippines though. C2 may have come north from South Wallacea with the Austronesian shuffle, and K may be a back movement from New Guinea (although it does seem to be in the wrong place for this to be so). To me they are the two most interesting haplogroups in the map. The other are all definitely more recent than the Paleolithic, and probably part of the Austronesian shuffle.

"Because they do not look Aborigen Taiwanese. As simple as that".

It's not actually simple at all. The Austronesians are by no means exclusively Y-hap O1 and O2. Certainly it looks as though O1 moved south to the Philippines from Taiwan, and kick-started the Austronesian expansion, but beyond the Philippines we find very little O1. To the south the Austronesians are associted with both other O haplogroups.

"I am talking is about the first arrival of Austronesians to Philippines from Taiwan".

That is O1. Neither of the others.

"Can you make a difference between the core population and the expanded population, which may well be very different genetically?"

Obviously yes. The core Austronesians were Y-hap O1 but other haplogroups were taken up during the expansion. And that expansion is most unlikely to have been uni-directional, especially before it had built up a head of steam.

"Pointless. Messing around with words. Arguing about nothing".

No it's not. Both O2 and O3 could easily have been introduced to the Philippines after Y-hap O1. In fact are most likely to have been so. O3 almost certainly does not represent a pre-Austronesian haplogroup in the Philippines.

"which indicate an earlier presence of haplogroups C-RPS4Y and K-M9 in the Philippines"

Maybe not. That is why I consider those haplogroups to be the most interesting in the study. They may be pre-Austronesian there, but they may not be. They too may be outsiders.

They may not be indigenous to the Philippines though. C2 may have come north from South Wallacea with the Austronesian shuffle, and K may be a back movement from New Guinea (although it does seem to be in the wrong place for this to be so).

By region, I meant the wider region consisting of Oceania, Australia, New Zealand and parts of Southeastern Asia including all of the Malay Archipelago, shortly all of the regions that more or less carry the genetic imprint of Australoid and/or Negritoid populations.

I've checked my data and see I was wrong there. Y-hap O1 does indeed spread down to Tenggara. It then swings east to a little bit in the Moluccas, and even a small amount out as far as Western Polynesia, and west to Borneo, Java and Sumatra.

"To the south the Austronesians are associted with both other O haplogroups".

The main O haplogroup in the Austronesian-speaking people of the Pacific is O3a. O3 is the most common haplogroup all through China, Vietnam, Malaysia and Sumatra. Therefore it's unlikely to be early, pre-Austronesian, to the Philippines. The O haplogroup in Madagascar, and which presumably carried the Austronesian language there, is O2a.

"By region, I meant the wider region consisting of Oceania, Australia, New Zealand and parts of Southeastern Asia including all of the Malay Archipelago, shortly all of the regions that more or less carry the genetic imprint of Australoid and/or Negritoid populations".

So you agree that Y-hap O is an immigrant to the region?

By the way Maju. I was studying evolution, genes and subspecies formation long before you were born.

I think the "C-RPS4Y" in the charts of this paper is actually C*. We can see that the majority of Polynesian Y-DNA shown in the map are "Others" which should be C2, and "Others" in Australia are mostly C4.

Negrito K-M9 could be k-M526* and Filipino O3* could be mostly O3a3-P201*, according to Karafet's 2010 paper on Indonesian Y-DNA.

I am confused by the mention in some comments about 'malay Filipinos' which I interpret to indicate mainstream Filipinos. The Philippine map is showing information ONLY from what we call "cultural minorities" or "indigenous communities".

'Malay Filipinos' means non-Negrito Filipinos generally. The Malays almost certainly are associated in the Philippines with Austronesian-speaking people. As you say, they are now a majority, mainstream if you like.

"The Philippine map is showing information ONLY from what we call 'cultural minorities' or 'indigenous communities'".

There are no data for the 'Malay Filipinos' in the map, are there? I do not see data for Tagalogs, Ilocanos, or Visayans. I am presuming that the discussion here is limited to Philippine ethnic minorities who actually moved into the archipelago much earlier.

The ethnic minorities represent early inhabitants of the archipelago and are understandably genetically diverse. I came across this looking for mainstream Filipino haplogroups and the diversity between regions.

With the refinement of Y-DNA K's phylogeny we can now see that Philippines K would be k2b1c-P378, confined to the Philippines especially in the Aeta. No other K outside the Philippines would belong to that branch. Other K1b1s are K1b1a, basically confined to New Guinea/Melanesia with a presence in Australia; K2b1b, from Borneo; and what we could call K2b1d or M, from eastern Indonesia and Melanesia. The C is still a mystery but could easily be C1b1a2-B65, found on the nearby island of Borneo, rather than being Wallacean C1b2a-M38. And certainly not Australian C1b2b-M347. It is also unlikely to be any C2-M217 branch.

Old Blog Archive

Dienekes' Anthropology blog is dedicated to human population genetics, physical anthropology, archaeology, and history.

You are free to reuse any of the materials of this blog for non-commercial purposes, as long as you attribute them to Dienekes Pontikos and provide a link to either the individual blog entry or to Dienekes Anthropology Blog.

Feel free to send e-mail to Dienekes Pontikos, or follow @dienekesp on Twitter.